Scientific large language models: A survey on biological & chemical domains

Q Zhang, K Ding, T Lv, X Wang, Q Yin, Y Zhang… - ACM Computing …, 2024 - dl.acm.org
Large Language Models (LLMs) have emerged as a transformative power in enhancing
natural language comprehension, representing a significant stride toward artificial general …

[HTML][HTML] Teaching AI to speak protein

M Heinzinger, B Rost - Current Opinion in Structural Biology, 2025 - Elsevier
Highlights•Protein Language Models (pLMs) tap into large unlabeled data to transform
protein science.•pLMs boost protein structure and function prediction performance and …

Sequence modeling and design from molecular to genome scale with Evo

E Nguyen, M Poli, MG Durrant, B Kang, D Katrekar… - Science, 2024 - science.org
The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an
organism's function. We present Evo, a long-context genomic foundation model with a …

[HTML][HTML] Are protein language models the new universal key?

K Weissenow, B Rost - Current Opinion in Structural Biology, 2025 - Elsevier
Protein language models (pLMs) capture some aspects of the grammar of the language of
life as written in protein sequences. The so-called pLM embeddings implicitly contain this …

Multimodal AI/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases

W DeGroat, H Abdelhalim, E Peker, N Sheth… - Scientific Reports, 2024 - nature.com
Cardiovascular diseases (CVDs) are complex, multifactorial conditions that require
personalized assessment and treatment. Advancements in multi-omics technologies …

A long-context language model for deciphering and generating bacteriophage genomes

B Shao, J Yan - Nature Communications, 2024 - nature.com
Inspired by the success of large language models (LLMs), we develop a long-context
generative model for genomes. Our multiscale transformer model, megaDNA, is pre-trained …

Artificial intelligence for omics data analysis

Z Ahmed, S Wan, F Zhang, W Zhong - BMC Methods, 2024 - Springer
Recent technological advancements have vastly improved access to high-throughput
biological instrumentation, sparking an unparalleled surge in omics data generation. The …

Learning the language of DNA

CV Theodoris - Science, 2024 - science.org
With a vocabulary of just four nucleotides, the language of DNA encodes the fundamental
information needed to orchestrate all layers of regulation in a cell, from DNA to RNA and …

Programmable biology through artificial intelligence: from nucleic acids to proteins to cells

OO Abudayyeh, JS Gootenberg - Nature Methods, 2024 - nature.com
Programmable biology through artificial intelligence: from nucleic acids to proteins to cells |
Nature Methods Skip to main content Thank you for visiting nature.com. You are using a browser …

Improving viral annotation with artificial intelligence

ZN Flamholz, C Li, L Kelly - Mbio, 2024 - journals.asm.org
ABSTRACT Viruses of bacteria,“phages,” are fundamental, poorly understood components
of microbial community structure and function. Additionally, their dependence on hosts for …